The Choice
by KidKneeGirl
Summary: John Sheppard has to decide who lives Rodney or Elizabeth. COMPLETE. Please R&R thanks. Due to deman, I added more chapters to this story. Enjoy and please R&R. Thanks.
1. Chapter 1

The Choice

_Choose_.

Lt. Colonel John Sheppard blinked open his eyes. He was lying on his back, the coolness of the metal floor seeping through his jacket. He waited a moment, taking an internal inventory of his body, and finding nothing bleeding, broken or otherwise damaged, he carefully rolled to his side, propping his weight on his right hand.

_Choose_.

John glanced at his surroundings. He was in a window-less, door-less metal room. It was fairly large, but the absence of color was disorienting. He came to his feet, automatically checking for his weapons. Yeah, they were gone.

"Hello?" His voice should have echoed in the room, but instead, it fell flat, the sound dropping like a stone the moment it left his mouth.

_Choose_.

A sexless, lifeless voice intoned the word, and John paced back and forth, running hand through his spiky hair. Choose? Choose what?

"Ummm….My name is Lt. Colonel John Shep…" His attempt at an introduction was interrupted by the same voice, the same command.

_Choose_.

As John turned slowly within his cell, the wall on the far side seemed to drain away. He walked over, and cautiously touch the surface; it remained solid to the touch. 'Some kind of weird window,' John thought. He gazed through it and felt his heart stop. In the next room, huddled together, were Rodney McKay and Elizabeth Weir.

As John watched, a light from overhead suddenly enveloped the two, and Rodney's face constricted in terror. John beat his fist against the window, trying to get either McKay's or Elizabeth's attention, but they didn't seem to be able to hear him.

_Choose_.

John whirled around, his hands clenched into fists. "Choose what?" he yelled, his green eyes angry.

_One will live. One will die. Choose._

John felt his stomach clench at those words. It was a nightmare come true. He was being forced to decide which of his two best friends – the two people he cared about most in this world – would live.

"Look, whoever you are, I can't do that." John started walking the perimeter of the room, looking desperately for something – anything - that would allow him to escape. But the walls were seamless, even at the floor and ceiling. As he strode back to the window, he could see Rodney speaking quickly to Elizabeth. She was shaking her head at his words, her eyes fearful.

_Choose. Or both die._

John raised his hands, pressing them against the window.

"Rodney! Elizabeth! Can you hear me?" Nothing. The two remained within the confines of the light, Rodney's hand grasping Elizabeth's.

_Choose. Or both die._

"I can't! Don't you understand?" Shaking, he gazed at his friends. How could he choose between them?

Elizabeth. Brilliant and beautiful, she was always there to back him up, no matter what mess he had managed to create. He admired and respected this woman more than he thought possible. Over the last two years, he had learned her likes, her quirks, her moods, her laugh. Her need for a cup of coffee before she spoke to anyone. The way she lifted an eyebrow one way when she was amused, another way when she was annoyed. He knew her boundaries, knew when to push and when to walk away. She was vibrant, alive and, most importantly, his friend.

Rodney. A genius, yes, but so much more. By becoming a member of John's off-world team, John had seen that behind the acerbic wit and incessant complaints was a man who put everyone's interests before his own. Many saw Rodney as a cold-hearted, self-centered scientist, but John knew Rodney better than that. He was selfless, often brave, sometimes funny, and always reliable. Loyalty was Rodney's greatest strength, not his brains. The two men seemed worlds apart at first glance, but Rodney was the friend – the brother - John never had.

_Choose_.

Elizabeth had leaned in to Rodney, and John watched as McKay pulled her into an embrace. He felt his heart breaking as the scientist held the expedition leader, doing his best to comfort her. Rage suddenly filled John at the thought of condemning one of these two people to death.

"I choose _me_," he screamed at the formless voice. "Not Rodney, not Elizabeth. I choose me. Kill me and let them go!"

_That is not an option. Choose one; the other dies._

John sank to his knees, his hands braced against the window. Choose one. The other dies. Helplessness and grief welled up within him. How could make this choice?

He needed Elizabeth. He was well aware of his evolving feelings for the beautiful leader. Friendship was becoming something more, and although they avoided any conversation about intimacy, their teasing and flirting often left John breathless. Many times the silences between the two were filled with electricity, heavy with want and need. John would retreat to the gym, focusing his energy on invisible enemies, doing his best to ignore the passion thrumming through his veins. Neither he nor Elizabeth were ready to acknowledge their increasing attraction, but John knew, one day, he would have to tell the woman that he was falling in love with her. And that he wanted more.

Atlantis needed Rodney. John knew that without Rodney McKay, not only would there not be an Atlantis, there wouldn't be a John or an Elizabeth, either. The man had saved everyone so many times that it had become something of a joke. Still, John was well aware that Rodney was the reason they remained in the Pegasus galaxy, discovering new technologies and making alliances. Radek Zelenka may have the knowledge, but even the Czech scientist turned to Dr. McKay when the shit was really hitting the fan. As did everyone else - John included. The man had a gift for pulling rabbits out of battered hats. Yes, Atlantis needed Rodney, even more so than it needed John, or even Elizabeth.

_Choose_.

He squeezed his eyes shut, hating the voice and the decision it was forcing upon him. He was more protective of Rodney and Elizabeth than anyone else in the world – in the universe, even. How could he condemn one of them to death? How would he look the survivor in the eye, knowing he had become the executioner of the other?

For there was the relationship between Elizabeth and Rodney to consider. John knew that the three of them – the soldier, the negotiator and the scientist – had formed an unlikely leadership. Atlantis thrived because of the three of them, the balances they had worked hard to achieve, the respect they each had for one another. Yes, John had formed a strong bond with both Rodney and Elizabeth, but the two of them had also become close. John would often find the taciturn physicist sharing a cup of coffee with Elizabeth, the two of them deep in an earnest discussion. There was love there, and admiration. John knew that as well as he knew his own name. Rodney and Elizabeth and John. All three were bound together by necessity, and by choice. To lose one member of their triumvirate would be devastating.

_Choose. Now._

John bowed his head, his mind racing, his heart pounding. He couldn't do this. He couldn't make this decision. But could he let both of them die because he feared his choice was the wrong one? Or because he would carry the guilt of his choice for the rest of his life? Who should live? Who should die? John shuddered; this was going to kill him.

_Choose. Now._

He closed his eyes. Tears made their way slowly down his cheeks. He drew in a deep breath. His heart cold, his body numb, he reopened his green eyes and gazed at his two friends. They were still entwined, Rodney's cheek pressed against Elizabeth's hair, the scientist murmuring to the leader. Her own eyes were glazed with shock, and her hands were clenched in Rodney's jacket, holding him tightly.

_Choose. Now._

In a voice that seemed dead, John softly whispered a name. A moment later, he saw the blood, the pain, the fear.

One lived.

And one died.

oOo

John Sheppard woke with a cry, his lungs desperate for air, his heart pounding in his chest. Sweat streamed from his body, and his bedding was knotted into a ball at the foot of his bed. Outside, stars winked in the night sky.

He sat up, gripping the mattress as he tried to come fully awake. It was only a dream; a nightmare. Nausea rolled through him as he remembered, and he staggered to the window, throwing it open and dragging in huge gulps of the cool night air.

He knew that sleep was not going to return tonight. Memories of the dream lingered on his mind, and he shivered. He had been forced to choose between Rodney and Elizabeth. And he had done it. Once more his stomach rolled, and John fought back the urge to be sick.

He wondered if he would be able to look either Rodney or Elizabeth in the eye when morning finally came.

He wondered if his fear, his need, his love for both of them would ever lead him down to this moment – a moment where a choice had to be made. A moment where an action of his, a decision of his, would lead to one of his friends living, the other dying.

He wondered if, like in the dream, he could actually make that decision.

And, he wondered, would he survive the outcome?

The End

A/N – Okay, so who did John choose to live? And why? All thoughts, opinions and ideas are appreciated.


	2. Chapter 2

A/N – I hadn't planned on adding any chapters to my original story, but a few

people wanted to know who was picked (see Chapter 1). I still haven't

decided myself, so I guess we'll all have to wait and see. Thanks for all your reviews and input. KKG

The Choice

Chapter 2

The morning meeting was coming to a close, and Elizabeth stifled a yawn. She sat in the conference room, listening as Carson Beckett, the chief medical officer of Atlantis, gave an update on the status of the infirmary. Normally, she enjoyed listening to Carson; he had a wonderfully dry sense of humor, not to mention that charming Scottish accent. But today, she was worried. She gravely eyed Colonel Sheppard, who was in his customary seat directly to her right. He had arrived late this morning, dark circles ringing his eyes, his hair beyond messy. He had sat down, barely acknowledging her existence, let alone anyone else's, and sat glumly sipping a cup of tepid coffee.

This wasn't good. John Sheppard was normally a buoyant, happy-go-lucky kind of guy, who managed to make wry little jokes even when they were under attack by hordes of Wraith. That he sat so still and cold, apparently ignoring everyone around him, caused a flutter of concern to course through Elizabeth.

Dr. Beckett finished delivering his report, then sat down. Next to him, Rodney was impatiently drumming his fingers on the table, and Elizabeth had to bite back a smile. She and the physicist were scheduled to go off-world later on that day, hoping to establish a better trade agreement with a galactic neighbor.

"Is that it?" Elizabeth glanced around the room, her gaze stopping at John, who still seemed lost in his own thoughts.

"Okay, well thanks everyone. See you next Monday." Elizabeth remained seated as the rest of the senior staff rose from their chairs and, in groups of two or three, exited the conference room.

"Dr. Weir?" Rodney rose from his seat and approached the expedition leader. If he noticed that John remained seated, the Colonel's green eyes focused on the table top, he made no mention of it.

"Yes, Rodney?" Elizabeth looked at the scientist, her sharp eyes taking in the tell-tale signs of excitement that the physicist barely tried to hide. A small smile danced around Rodney's normally frowning mouth, and his blue eyes held a glimmer of enthusiasm. Reports from P2X966 had indicated an abundance of a fairly rare mineral, and Rodney was itching to investigate. Elizabeth returned his smile, already knowing his question.

"Two o'clock, right?" Rodney asked, and Elizabeth nodded her head.

"Yes. Major Lorne and his team will be escorting us to P2X-966. I have a couple of things that I have to do first, but then we can go…." Elizabeth was cut off as John suddenly slammed both hands on the table, and rose to his feet.

"NO!" Tension radiated from the Colonel as he glared Elizabeth and Rodney, and the scientist resisted the urge to step back. John was his friend; the Colonel would never do anything to hurt either Elizabeth or himself. Still, Rodney was shocked at the heated look the Colonel shot at the both of them.

"Excuse me, Colonel?" Elizabeth's voice had a sharp edge to it, and Rodney flinched. Usually he was on the receiving end of Dr. Weir's anger. While it was refreshing to have her ire directed at someone else, he still grimaced at her tone.

John paused, taking several deep breaths. Then, in a controlled tone, he replied, "I said no. Neither of you are going anywhere."

"The last time I checked, Colonel Sheppard, I didn't have to get your permission to leave Atlantis." Elizabeth's words were clipped and ragged, and Rodney frantically tried to send John a silent warning, waving his hands behind the leader's head. John ignored Rodney, keeping his own glare focused on Elizabeth. She returned his gaze coolly, waiting for an answer.

A few frigid moments passed between the two, then John reached down and keyed his comm.

"Major Lorne? This is Sheppard. Under absolutely no circumstances are Dr. Weir or Dr. McKay to leave the city until further notice. Is that understood?" Elizabeth and Rodney opened their mouths to protest, interrupted by the confused voice of Major Lorne.

"Sir? We were scheduled to go off-world this afternoon. Dr. Weir has a trade meeting…" Lorne got no further. Rodney had stepped forward, his bewilderment transforming into anger.

"Now, wait just a minute, Sheppard!"

"Colonel! Under whose authority are you making these orders?" Elizabeth had planted her hands on her hips, her face dangerous.

John held the angry looks of Elizabeth and Rodney as they voiced their own dismay. Memories of his nightmare echoed through his brain, and he closed his eyes for a brief moment. The two of them abruptly quieted as pain flowed across John's face.

"John? What's going on?" Elizabeth reached out and placed a warm hand on his arm, her anger transforming into concern. Rodney froze as John shrugged off Elizabeth's touch.

"I can't…I can't tell you. But neither of you are to leave Atlantis, at all, for any reason whatsoever. If you disobey me, I'll throw you both in the brig. Am I making myself clear?" John's tone was firm, and without waiting for an answer, he stalked from the room, leaving Rodney and Elizabeth to gaze at each other in bewilderment.

"Can he do that?" Rodney asked. Elizabeth was staring at the door where Sheppard had disappeared, a frown on her beautiful features. She folded her arms across her chest, her hazel eyes worried.

"No. But more importantly, why would he want to?" Elizabeth asked softly. Rodney, his face troubled, gave a shrug of his shoulders, then plodded out of the room.

"What is going on, John?" Elizabeth whispered softly.

TBC


	3. Chapter 3

The Choice

Chapter 3

John stalked down the hallway, his mind on fire. He ignored the personnel that stepped out of his way, his memories of the dream consuming his thoughts. It was making him crazy.

He had forgotten Rodney and Elizabeth were going off-world today. Normally, he would have escorted them to P2X966, but he had been scheduled to meet with Kate Heightmeyer. He had put off seeing the psychologist three times, and Carson had warned him that if he cancelled this time, he would not be allowed to go off-world again. That order had been accompanied by a poke in the chest, and a glare from the Scotsman. Resigned, John had agreed to let Major Lorne and his team go with Elizabeth and Rodney.

That was before the nightmare. Now, though, the thought of letting either one of them out of his sight was unnerving. John ran a hand through his hair, his feet slowing as reality descended. _It was only a dream_. The truth was, Rodney and Elizabeth would have been very safe with Lorne. P2X966 was an established trading partner; they had been friendly allies for more than a year now. There was no reason to expect any kind of trouble.

Still, John had felt a shudder creep up his spine when Rodney had queried Elizabeth about their departure time. John knew his reaction had been unreasonable, but it was all he could think of to do at the time. Elizabeth was bound to call him on his actions, and Rodney – he was never going to hear the end of the scientist's complaints.

John stopped walking. This wasn't going to work. He needed to figure this out, or he was going to lose his two closest friends. He already owed them both a huge apology for his actions this morning.

He glanced at his watch. He was to meet with Heightmeyer in a half hour. Maybe she could help him. John frowned; he disliked speaking with the psychologist almost as much as Rodney, and the thought of revealing his dreams to anyone was distasteful. But he had to do something. Heaving a deep sigh, he turned around, his feet leading him to Heightmeyer's office.

oOo

Kate Heightmeyer was surprised. Sitting in her office, his hands in his lap, his eyes unsettled, was Colonel Sheppard. He hadn't responded to her greeting, and instead, entered the room and planted himself in one of her chairs. Kate watched him for a moment, then took the chair next to him.

He was troubled; that much was apparent. His eyes wore dark circles, and he sat straight and still, his posture rigid. He flinched as she touched his shoulder, then gave her a sad smile.

"Colonel Sheppard. What's wrong?" Kate's soft inquiry caused him to tense up even more, and John felt like he was going to shatter. He didn't answer for a long moment, then gave a deep sigh.

"I…I had a dream last night. A nightmare, really," he began hesitantly. Out of the corner of his eye he could see Kate nod. Nightmares were the number one problem the people of Atlantis complained about, even more so than the food.

"Do you want to tell me about it?"

John leaned back into his chair, his hands still clenched tightly together. Slowly, hoarsely, he began speaking, forcing the words out as he described the horror of last night.

"They…it.. whatever…made me choose! I didn't think I could do it……but I did." Tears were streaming down the Colonel's face, and he choked back a sob. His hands rubbed at his forehead, like his was trying to push the memory out of his mind. Kate stared at him thoughtfully for a moment, then reached out and laid her hands on his.

"You've had nightmares before, Colonel Sheppard. Yet this one seems to be affecting you more than any of the others. Do you know why?"

John nodded his head. "It was so real. I could see their fear. I could hear…." John trailed off, misery etched on his face. Kate sat back, a frown on her face.

"Colonel. I'm going to break a cardinal rule here, but I think it's necessary." She waited as he raised his head, his green eyes searching hers curiously. She got up and went around to her desk, flicking on her computer. She leaned over and typed in a command, then turned the screen towards Sheppard.

"First of all, you're not alone. Almost everyone on Atlantis has complained to either myself or Dr. Beckett about having nightmares. It's a common problem."

John nodded slowly. Dr. Heightmeyer paused for a long moment, then reached down and hit a key. Words scrolled across the monitor.

"I want you to read this," Kate said. John hesitated a moment, then leaned forward, his eyes scanning the screen.

_Patient: Dr. Elizabeth Weir_

_Dr. Weir approached me this morning and asked if she could schedule an appointment. I could see that she was extremely distressed, and took her in immediately. She required a few moments to get her thoughts organized, but then proceeded to describe a nightmare she had the previous evening. _

_Apparently, the entire SGA-1 team, commanded by Lt. Colonel John Sheppard, had been killed. Dr. Weir acknowledged that she understood that it was only a dream, and that the team was not actually dead. However, she questioned her decision to have Colonel Sheppard and Dr. McKay be members of the team._

_When I pushed, she admitted that she had been considering re-organizing the team so as to keep both Sheppard and McKay here on Atlantis._

John's eyes widened as he read the report. He knew Elizabeth worried when they went off-world, but she fretted about all the teams. The fact that she wanted to effectively ground both himself and Rodney was disconcerting.

_Dr. Weir then recanted this statement, saying that she knew that both Sheppard and McKay would not want to remain on Atlantis, and, in fact, would probably make her life "a living hell" if she did order them to do so. She then spoke of her growing admiration for the two men, and revealed that she feared that without them, she would be unable to effectively run Atlantis. The fact that she had lost both men in her nightmare, as well as Teyla Emmagen and Ronon Dex, had rendered her extremely anxious. I reassured Dr. Weir that both Colonel Sheppard and Dr. McKay seemed more than capable to continue exploring the Pegasus galaxy, even if they did manage to get themselves into trouble._

John grimaced at the last statement. They didn't mean to find trouble; usually, it found them.

_Unfortunately, Dr. Weir's problem remains unresolved at this time. I advised her to try and speak with both Colonel Sheppard and Dr. McKay, and share her dream with them, but she refused, citing that they each had "enough to worry about without their boss dumping on them." We scheduled another meeting in three days. KH_

John stared at the screen for a long moment, feeling a rush of sympathy for Elizabeth. How hard it must be to see your colleagues, your friends, walk through the stargate, wondering if they would be all right, if they would return in one piece. Elizabeth rarely had the opportunity to go off-world, and John was perfectly happy if she never did again. He knew quite well how dangerous it was to leave the relative safety of Atlantis, and the thought of any harm coming to Elizabeth made his stomach clench. Now, it seemed as though she had the same reaction.

Kate was watching him carefully. She leaned over and typed another command into the computer, then swung the screen back towards Sheppard.

"Now read this," she said.

_Patient: Dr. Rodney McKay_

_Dr. McKay arrived for his weekly appointment on time. When I inquired as to how things were going, he stated that he was continuing to suffer from nightmares almost every night. He refuses to take the sleep-aid Dr. Beckett prescribed, stating that he would prefer to deal with his fears rather than avoid them. While I commended Dr. McKay for his attitude, I wasn't surprised. Dr. McKay relishes confrontation of any kind._

_He proceeded to describe his nightmare to me. In it, he was required to watch various people being killed by the Wraith. When I commented that his nightmares had changed, from having him be the victim to having others become victims, he reacted angrily. _

"_I preferred it when I was being tortured, actually. Watching John and Elizabeth suffer is much harder." We agreed that he despised feeling helpless, and that his growing affection for Dr. Weir and Colonel Sheppard were creating conflicting feelings. On one hand Dr. McKay enjoys the friendship and companionship he shares with the two. On the other, he fears that something will happen to either one, and he wouldn't "survive the loss" (his words)._

_Once again, Dr. McKay reiterated that he was considering resigning from the Atlantis project. This is the fourth or fifth time that he has admitted he was torn between remaining here on Atlantis or returning to Earth. He remains enamored with the city and the Pegasus galaxy, and is thriving with the relationships he has made here. However, his enormous burden of guilt after the deaths of so many of his colleagues, as well as his anxiety that he will be unable to "save the day" in the future often leave him depressed. He fears that his actions will result in injury or death to someone he cares deeply about. _

_Unfortunately, we ran out of time. I advised Dr. McKay to refrain to deciding on leaving Atlantis until he had more time to think about it. I also encouraged him to discuss his feelings with either Dr. Weir or Colonel Sheppard, but he refused, saying it was bad enough he was "spewing" his thoughts to me. We agreed to meet at the same time next week. KH_

John was amazed. It had never crossed his mind that Rodney would even consider leaving Atlantis. If anyone belonged here, it was the grumpy physicist.

Kate gently pulled the computer away from John, then returned to her chair.

"I get your point, Doctor," John said quietly. And he did – he was not alone. Apparently, Elizabeth, Rodney and pretty much everyone else had the same fears, the same nightmares. The frightening thought was that here, in this strange and wonderful new place, your nightmares had a good chance of coming to life. John was familiar with the strong bonds that formed between soldiers in times of battle. Being isolated here, in a distant galaxy, with limited access to everything that was warm and familiar, had created ties between people who probably wouldn't have even given each other a morning greeting on Earth. Would John have befriended Rodney had he never come to Atlantis? Probably not. And he would have never had the chance to know the warmth and humor of Elizabeth, because he would have never met her.

John sat back in his chair and sighed. Kate stared at him for a moment, then spoke.

"Colonel Sheppard, you have an enormous protective instinct, especially for Dr. Weir and Dr. McKay. As the leaders of Atlantis, the three of you have formed an extremely close relationship. The thought of losing either one – permanently – is frightening." Kate Heightmeyer paused, watching as her words sank into John.

"You not only fear losing one of your friends, but actually having to move on without them. This relates to your "leave no one behind" motto. Unfortunately, after the incident with Lt. Ford, you realized that there will be times when people will be lost, and not only due to death. You feel you've failed Ford. You are afraid that one day you will also fail Dr. Weir or Dr. McKay, and your failure will result in their loss."

John nodded silently, realizing that in a few short sentences, Kate had summed up his entire psyche. He didn't know whether to be impressed or dismayed.

"John." Sheppard looked up, and saw the concern in Kate's eyes. "I think you need to talk to Dr. Weir and Dr. McKay. You need to tell them how you feel, tell them about your nightmare. All three of you have admitted that you fear losing the others. Keeping these feelings inside only gives fuel to the fear."

"But, how do I tell them about the choice I made? How do I tell them that I let one die?" John stood, his frustration making him pace the floor. He ran a hand through his hair, his green eyes tormented.

Kate shook her head slowly. "It was only a dream, John. They will understand that."

John paused, feeling cold. "I hope you're right."

TBC


	4. Chapter 4

The Choice

Chapter 4

Elizabeth was seated behind her desk, nearly obscured by the piles of paperwork. It seemed ironic to her that a majority of the work performed here on Atlantis was managed by computer systems, yet there still was an inordinate amount of paper generated. She stifled a yawn, then reached over to take a sip of coffee, only to find her cup empty.

"Need a refill?" John's voice startled her, and she dropped her cup to the floor.

He sauntered over, then reached down to retrieve the mug. He still seemed ragged, his green eyes tired and haunted. But he gave her a small half-smile before placing the cup carefully on her desk.

"Elizabeth, we need to talk," John said. She nodded, then walked over to the door, closing it firmly. She turned, and folded her arms across her chest. Her eyes were wary and concerned.

"What happened this morning, John?" She remained leaning against the door, and John heaved a huge sigh, then sat against the corner of her desk.

"Look, I'm sorry. I overreacted, I know. But, I…..I had a nightmare last night, and …" He trailed off, searching for the words to describe the jolt of fear he felt when she and Rodney started discussing their off-world plans.

Elizabeth's frown transformed into understanding. She couldn't remember the last time she had a good nights sleep, even tossing and turning when her body was exhausted. That John had been so affected by a dream meant that it must have been horrific.

She approached him, letting her hip brush his as she moved next to him. Always, whenever she was next to this man, she felt safe and comforted. She hoped that her presence would have the same effect on him. He remained leaning on her desk, his head drooping as though the weight of the world was balanced on his shoulders. And, in many ways, it was. John took his responsibility as the protector of Atlantis and her people quite seriously. It was one of the reasons Elizabeth had forced the committee to promote him to Lt. Colonel. John had earned the rank, as far as Elizabeth was concerned.

"Do you want to tell me about your nightmare?" she asked softly, and she was startled to see real fear in his eyes.

"No, I don't, but Heightmeyer says that it will help if I do." Elizabeth's eyebrows raised; this nightmare had shaken him enough to make him see Kate. This was a first.

Slowly, hesitantly, painfully, John began speaking of his nightmare. Elizabeth could hear the anguish in his voice as he described his helplessness, his rage, at being unable to rescue either Rodney or herself. She could see his agony at being forced to chose one of them to live, and she felt a familiar shudder creep up her spine. She, too, had nightmares where her decisions resulted in someone being injured or killed.

John had stopped speaking. He took in a deep breath, trying to maintain control, and Elizabeth resisted the impulse to wrap her arms around the Colonel. Now wasn't the moment for comfort; now, she had to listen to him and remain the detached leader.

"I couldn't let you both die," John whispered. He finally turned to look at Elizabeth, and saw the sympathy in her eyes. He opened his mouth, to reveal who he had chosen, when suddenly, she left his side and paced the room. She paused and held up one hand.

"I don't want to know, John." Elizabeth clenched her hands into fists and let her arms drop to her sides. "I've had the same nightmare, and no matter what happens, no matter what decision I make, the result is the same. I wake up feeling guilty. Lost. Responsible."

John nodded his head, watching as she approached him and placed her hands on his shoulders.

"I just need to know that you did make a decision, John. That no matter how hard it was, you were able to make a choice." Her face was determined and John realized that as leader of this expedition, Elizabeth was required to make choices everyday, choices that could potentially lead to someone's death. He had known this all along, but, in the wake of this nightmare, the reality of their lives suddenly became apparent.

And the reality was, that for every triumph was a tragedy. Although life on Earth was every bit as tenuous as it was here on Atlantis, somehow, life here seemed much more precious, friendships more dear. Some of the stress had been relieved by the arrival of a ZPM, and by Colonel Caldwell and the _Daedelus_, but still, they were isolated, far from the familiar, extraordinarily dependent on each other. Everything was heightened here on Atlantis: fears, joys, relationships, losses. It was draining and exhilarating at the same time.

He gazed into Elizabeth's face, noting the lines around her eyes, the brittleness of her smile. Had he been able to choose between Rodney and Elizabeth?

"Yes. I was able to choose," he answered. She nodded her head, a thoughtful look on her face, then she enveloped him in a hug. Surprised, John stiffened for a moment, then feeling her warmth, he wrapped his arms around her and returned the embrace.

They remained entwined for a long moment, then Elizabeth stepped back, gently running a hand across his shoulder.

"I knew you could, John. That's all that matters." She gave him a quick, sad smile, then asked gently, "Are you okay?"

"Yeah. I guess Heightmeyer was right; talking does help." And, to his surprise, he did feel better. The nightmare, which had loomed so large and real, now seemed to be fading, drifting, dissolving into scattered remnants. John felt cleaner, lighter, and no longer smothered by his fear. He took in a deep breath.

"Wanna have dinner later?" he asked, his face still drawn but a slight twinkle in his eye, and Elizabeth smiled. This was the John Sheppard she was accustomed to, teasing and fun and so very handsome. She squelched her own fears of losing this man, and made a show of considering his offer.

"Well, seeing as you owe me for this morning, I suppose the least you could do is buy me dinner," she replied. He grinned, then turned to leave.

"I'll pick you up at 19:00?" He paused for a moment, waiting for her nod, then, his step noticeably lighter, headed down the hallway.

TBC


	5. Chapter 5

The Choice

Chapter 5

Dr. Rodney McKay was in a surly mood. He had bypassed impatient and grumpy hours ago, left irritated and grouchy in the dust, and had settled into argumentative and snappish. His co-workers had abandoned him, leaving him to stew in his own misery. Even Radek Zelenka, Rodney's second-in-command, who was accustomed to McKay's mercurial mood changes, had stomped out of the lab, muttering angrily in Czech under his breath.

Now, he peevishly tossed some Ancient device on to the table. He knew he was being unreasonable, but he was annoyed at Sheppard. Who did the Colonel think he was, preventing Rodney and Elizabeth from leaving the city? Rodney had been sure Elizabeth would confront Sheppard, and was amazed that she had remained silent. If he had tried to pull a stunt like that on her, he would have been lectured from today until doomsday.

"Rodney?" The scientist swung around, his blue eyes dangerous as they settled on John. Well, well, well. Rodney crossed his arms, his look challenging. He glared at the Colonel, noticing the fatigue on his face, the slight stoop in the man's posture. Rodney felt a small tingle of empathy flow through him, and forced himself to ignore it. He was angry with John.

"What can I do for you, Colonel?" Rodney spat out the words, seeing a slight flinch on John's face. He expected to feel satisfied, but, instead, regretted his harsh tone the second the words left his mouth.

John's own mouth drew into a straight line. He knew talking to Rodney would be much harder than dealing with Elizabeth, but the physicist wasn't making this easy.

"I wanted to apologize for this morning," John began. He raised his eyes, matching his gaze to Rodney's. The scientist had unfolded his arms, letting them fall to his sides, and started squirming uncomfortably.

"Well, you should be sorry. Elizabeth and I were looking forward to going to P2X-966. Do you have any idea how hard it is to coordinate our schedules?" Rodney paused, honestly not knowing if Elizabeth really was anticipating her time away from Atlantis. He watched as John's eyes shadowed, and mentally kicked himself. Something had happened to make Sheppard react the way he did, and Rodney cared about his friend. If he could only learn to curb his own tongue, things would be so much easier.

"Look, Rodney, I…. I had a nightmare last night, and it really screwed with my head. When you started talking to Elizabeth about leaving Atlantis, I just…freaked." John wandered over to one of the chairs, and sat down, running a hand through his hair.

Rodney remained silent. A nightmare. Inwardly, he shuddered. His own sleep was invaded on a regular basis by bad dreams. Dreams of Wraith, dreams of Genii, dreams of pain, and death and loss. Rodney worked himself to the point of exhaustion for three reasons: one – it was his job, two – it was a habit, and three – it kept him from dreaming.

Awkwardly, Rodney approached John. "Do you want to talk about it? The nightmare, I mean." He watched as John closed his eyes briefly, then glanced up at the scientist.

Once more, John spoke of being forced to make a decision, forced to watch as one of his closest friends was murdered. Rodney listened, his body growing cold as Sheppard described a nightmare that was eerily similar to his own.

"I had to choose, Rodney. I just couldn't let you both die, just because I didn't want to make a decision. It was really…..hard." John's voice had dropped to almost a whisper, and, without realizing it, Rodney had sat down next to the Colonel, wanting to offer the man some comfort.

"Been there, done that," Rodney quipped. He gave John a wry grin, but there was no amusement in the scientist's blue eyes. Only a look of profound sadness, and understanding.

"Look, John, I'm sure Elizabeth told you that we all have these dreams. It comes with the territory." Rodney paused, making a decision, then softly added, "You know, some of mine have been so bad that I've thought about leaving Atlantis."

John froze, surprised that Rodney had shared this secret with him. He watched as a myriad of emotions crossed the scientist's face.

"There are lots of reasons for me to stay, but the most important one is…well, I've grown used to having you guys around – even Ronon. Even if I felt safer on Earth, I'm not sure I would be as…..happy," Rodney added.

Happy? Rodney? John refrained from chuckling. If Rodney was happy here on Atlantis, John wondered what he was like on Earth. Yikes.

McKay got up and started pacing the floor. His brow was furrowed, his hands twitching, and John recognized the signs of a decision being made. He waited, and a few moments later, Rodney paused in front of him.

"Colonel, I want you to make me a promise," Rodney said. John merely raised an eyebrow, not committing to anything.

Rodney plunged ahead, his voice quick and sharp. "I want you to promise me that if you ever _really_ have to decide between me or Elizabeth, that you choose Elizabeth to live. Got that?"

John sat in shock for a long moment, then slowly shook his head. "No, Rodney, I can't do that." The Colonel stood, staring steadily at the agitated scientist. "You just don't get it, do you?"

McKay's eyes were clouded and angry, and John realized he had better tread carefully. Deliberately choosing his words, he rose and approached Rodney.

"You are my friend, Rodney. As difficult it is to believe, I like having you around. Even if you weren't a genius, I would still want you as my friend. God only knows why," John said wryly. The scientist stared back, an look of incredulity on his face.

"Umm…well…thanks. You too. I mean…you know what I mean, right?" Rodney's voice held a hint of desperation, and John shook his head as he smiled. Some genius.

"Yes, Rodney. I know what you mean." He watched McKay's shoulders relax, although the scientist still looked pensive.

"Look, let's just hope that we never have to make that choice, okay? After all, it was just a nightmare," John said, trying to inject a little lightness into his voice. Thankfully, Rodney just nodded, releasing a sigh as he ran a hand across his face.

"Are we good?" John asked, and Rodney gave him a small, crooked smile as an answer. Relief spread through John, and he realized how much he would regret losing Rodney as a friend.

"Look, I have work to do, so why don't you go and bother someone else for awhile?" Rodney said, turning back to his Ancient device. John paused long enough to rest his hand on the scientist's back, silently thanking him, then turned and left the lab.

TBC


	6. Chapter 6

The Choice

Chapter 6

Lt. Colonel John Sheppard shivered in the cool breeze. Above him, stars blinked and twinkled in cadence to the lap of the ocean. It still seemed weird to not have a moon shining above on nights like this. But he was getting used to it.

He leaned forward, resting his arms on the metal railing of the balcony. He had left Elizabeth a few minutes ago, after sharing a fairly edible dinner and some light conversation. Neither of them had mentioned this morning, or nightmares, or responsibilities. Instead, they shared funny stories and laughed and ate. John felt like he had actually managed to banish the events of the day from his memory, and had returned to his room, his heart light and his mind at peace.

Still….he was a bit nervous about going to bed. Falling asleep. And dreaming. What if the nightmare came back, with all the horror and guilt and pain? God knows he didn't want to relive it night after night.

Elizabeth had reminded him that if he needed to talk, he was to call her, no matter what time it was. He had agreed, but, now, he wondered if he really would trouble her, wake her in the dead of night, needing her comfort, her compassion, her quiet reassurance that everything was still okay. A part of him was uncomfortable with the idea of revealing his weaknesses and fears to another – especially Elizabeth. He preferred maintaining his image of a strong protector.

But Kate Heightmeyer had been right about one thing – talking did seem to help. There was something about sharing your fears, and realizing that almost everyone else suffered the same as you did, that somehow made it a bit easier to bear. And, he had to admit, if he was going to talk to anyone, it would be either Elizabeth or Rodney.

Thinking about the physicist, John felt a tremor of worry. He would have to figure out a way to get McKay to open up a bit more; it bothered John that Rodney still considered leaving Atlantis. Whether Rodney liked it or not, he was needed here. All three of them were.

John's dream returned to him, and the memory of the decision he had been forced to make. He had watched, his heart breaking, as Rodney McKay had cried out in pain, his anguish a living thing, as Elizabeth had sagged in his arms, blood spilling from her chest. Within moments, she had been dead, and John could see Rodney screaming her name over and over. Finally, the scientist had dropped to his knees, cradling the body of the expedition leader, tears of rage pouring down his face. Rodney had turned to the window, turned to John, loss and confusion and desolation in the scientist's blue eyes.

'Why?" Rodney had asked, although John couldn't hear his voice. He shuddered as he recalled that moment. Now, hours later, and awake, and fully aware that it was all a dream, he still found himself cringing at the accusing look in Rodney's eyes, praying that the scientist couldn't see through the window, and realize that John was responsible for murdering Elizabeth.

Sheppard pulled in a sigh. Elizabeth had known what his decision was – and had approved. Rodney, too – or he would have never insisted that John select Elizabeth. Somehow, in his eyes or by his choice of words, they had figured out who the protector of Atlantis had chosen to live. Even if it was only in a dream.

John closed the door to the balcony, and sat on the edge of his bed. How did that old saying go? Even if you decide not to choose, you still have made a choice. Or something like that. When he made the decision to return to Atlantis, most of it was based on the fact that he would be accompanied by Rodney McKay and Elizabeth Weir. If they hadn't returned, John wasn't sure if he would be here now.

Hence his nightmare; what would he do if either one was lost or killed? And what if he was the one ultimately responsible for their death? Could he move on, accept the guilt, deal with the aftermath? Or had he become so reliant on McKay's last-minute brilliant ideas, or Elizabeth's cool and calm in the midst of chaos, that to lose one of them was to lose an irreplaceable part of himself? John shook his head. He didn't want to know.

John undressed, crawled under his bedcovers and mentally dimmed the lights. He closed his eyes, relaxing, listening to the sounds of Atlantis at night. As sleep started to overcome him, he vowed to keep everyone on Atlantis, but especially Rodney McKay and Elizabeth Weir, safe and healthy. If it came down to it, he would give his own life to make that happen. 'That's my choice,' he thought.

And John Sheppard slept.

The End

A/N – Yeah, yeah, I chose Rodney to live. Like most of you, I really do believe the man is somewhat irreplaceable. Thanks for all the kind feedback and ideas. KKG.


End file.
